The Third Sect
by Janiqua
Summary: Crossover with Atlantis and Final Fantasy VII, though you need no experience with Final Fantasy to read this story. Sheppard and his team discover an Ancient colony, but the humans living there are certainly not Ancient, and as for the Wraith Queen...
1. Prologue

**Author's Note:**I've actually had this idea in my head for a long, long time. I know I should be working on other things, so much so that I don't know if I'll finish this one, but I can't keep from writing it any longer and my brother's pestering me to do it, so here it goes…

**Disclaimer:** I do not own Stargate. I do not own Final Fantasy.

**Warning:** I have no qualms whatsoever about throwing in spoilers for both Stargate and Final Fantasy. If you don't want to be spoiled, I'd advise you to read something else.

**Invitation:** This is an Atlantis fanfiction. It's about Sheppard, his team, and Daniel Jackson, because I couldn't resist writing in my favorite character. Anyway, you don't need to have any experience with Final Fantasy to read this story. I'll explain everything and so I invite everyone who loves Stargate to delve right in. Don't forget to leave a review!

**ooooooo**

**Stargate Atlantis  
Final Fantasy VII  
Stargate SG-1**

**ooooooo**

"**The Third Sect"**

**ooooooo**

_Thousands of years ago, a powerful race of beings known as the Alterans flourished throughout the universe. They were the Gate Builders. They were among the most advanced civilizations history ever saw. However, like so many such races, they one day found discord amongst themselves. They disagreed on how to wield their power. They divided… and so went their separate ways. The Ancients, the Ori, and a third sect, small, passive, and quickly forgotten. The Cetra. Itinerate by nature, they moved from one planet to another, unable to find a permanent colony. They grew to miss the rest of their people and gradually yearned to return to their great cities. The Promised Land. But their destination proved elusive. They could not reach or even find their home. Plagues were in abundance. Flying cities were easily lost. The universe is very vast. _

_The Ancients themselves remained unaware of their cousins' plight. A war had broken out against the Wraith and nothing could distract them from the fight they were losing. Over time, the Cetra grew weary of their never-ending search and settled on a world called Gaia. There, they found a semblance of happiness, living closely to and in harmony with the Planet itself. Some even forgot about their heritage… forgot entirely. Their descendants became the humans who nearly led Gaia to disaster… for there came a Calamity… a Calamity from the Skies… a mutated Wraith Queen known as Jenova… and she is planning a terrible reunion…_

**ooooooo**


	2. The Mission

**ooooooo**

The city had definitely been abandoned, that much was obvious.

Stepping through the Stargate, Colonel John Sheppard took in what appeared to be a barren wasteland and knew without a doubt, had he been in the inhabitants' place whenever they'd faced whatever the hell it was they'd faced, he more than likely would have abandoned it too. The trees all seemed lifeless. The ground was blanketed in gravel. Many of the buildings were either built or carved out of granite, which made for a rather drab environment indeed. Everything was colorless. A bit blustery. Hardly anything special.

Carrying himself at ease, he sauntered after Rodney McKay who was already marching towards whatever power source they were chasing this time. Head bent over a hand-held Ancient scanner, the overeager scientist was muttering to himself about life signs and energy readings. Apparently, according to their earlier briefing back in Atlantis, the planet was still occupied, but not anywhere near the gate and hopefully they wouldn't find themselves making contact with any of the locals anytime soon. All they wanted was the power source and if they could get to it and back again without attracting unwanted attention, Sheppard would be more than prepared to call this mission a success.

"I still believe this to be a bad idea," Teyla said, gravel crunching beneath her feet as she followed after the men, keeping an eye on the horizon. Sheppard could just make out the tree line ahead of them and it looked every bit as dead and decrepit as the rest of the city's vegetation. He sighed; 'ominous' was the word he'd use to describe this place and Teyla wasn't even finished yet. "Claiming a power source for ourselves before making contact with the people we know populate this planet is nothing short of stealing."

"Oh, come on, we've been through this a hundred times already!" Rodney stopped short and looked back at her in poorly disguised impatience. "If we want to be able to cloak Atlantis _while_ powering our shields, we need more of the one thing we're currently limited on. Power. Power these people might possess and yet aren't even capable of comprehending."

As much as it hurt his pride, Sheppard couldn't help but agree. He generally preferred siding with Teyla in these matters, particularly since Rodney had a nasty habit of completely disregarding those pesky ethical dilemmas that always seemed to follow scientific research, but unfortunately in this case subtly was something of a necessity. "Colonel Carter gave the go-ahead only because there's no one living in this city. We've never encountered a populated world that's not centered on an active gate before, at least not in the Pegasus Galaxy. Considering the Cullings, it's a miracle these people have advanced as far as they have."

"Advanced civilizations don't like the idea of extraterrestrials, believe me, I know," Rodney went on, speaking rapidly in a single breath, as if to save a crucial amount of time. "They'd rather be the center of the universe and anything that challenges their naïve, preconceived notions is viewed as imminently threatening. In all probability, since no one's watching the gate, they've either forgotten about it or don't care about it, in which case, our taking the power source won't affect them. I mean," he smiled haughtily, "if they've forgotten about it, what they don't know won't hurt them, right? And if they don't care about it, the fact they aren't using the power source for themselves clearly suggests they have no need of it. Not like we do."

"Of course we'd ask nicely," Sheppard added. "But if these people don't know about the gate, we've no way of knowing how open they'll be to the possibility of aliens. They might get hostile, in which case negotiating for supplemental power will be the very least of our worries. It's best to extract it before making any contact. Best for both worlds." Teyla regarded him uncertainly, but Ronon seemed satisfied. He casually slung his energy pistol over his shoulder and motioned for them to get on with it.

"If we're going to do this, let's do it fast," he said. "Before someone shows up."

Rodney scoffed. "Please. There's no one around for miles." Ronon and Teyla both glanced at him, their expressions unmistakable. Ronon didn't like being contradicted and Teyla didn't share the scientist's conviction. Their missions had a tendency of going horribly wrong and they couldn't afford being overconfident, not when they were walking headfirst into unknown territory on a planet inhabited by unknown people. They were prone to facing any number of unpleasant surprises and that was about the absolute last thing they wanted right now. Rodney must have recognized this for he tossed up his arms, frustrated but accommodating. "Fine." And with that, he turned his attention back to his scanner and continued on his strut away from the Stargate, the rest of his team following gradually behind.

The white sun blazed brightly in the sky overhead. After awhile, Sheppard put on a pair of sunglasses in attempt to relieve his eyes. The farther into the city they went, the more wearisome it became. As Rodney had said, and as he had first intuited, the place was empty, deserted and dismal. There was nothing to catch one's eye or interest. Crumbling edifices, archaic pillars, all rock, no art, he could well imagine even an archaeologist would get bored with the dump sooner or later. But then again… he wasn't an archaeologist, was he?

Rushing after Rodney and falling into place beside him, Sheppard wasted no time at all inquiring after a certain member of the infamous SG-1. "You think Dr. Jackson might want to check this place out? Get a real feel for the Pegasus Galaxy during his stay?" Rodney looked up from his scanner and though he didn't deviate from the path they were on, he took a long moment to really chew on the Colonel's question. Meanwhile, their curiosity aroused, Ronon and even Teyla kept up with their companions in order to eavesdrop on the conversation. Lately, anything that had anything to do with the archaeologist attracted their attention, for they both had yet to meet him.

"I don't know," Rodney said at last. "Maybe. Dr. Jackson's more fascinated with the city, I think, than with the actual galaxy. I mean he's been going off world for more than…" he waved around his left hand while grasping for a number, "ten years now." Sheppard whistled, but Ronon rolled his eyes, unimpressed. Rodney didn't notice. "After ten years, don't you think planets start blending together? We've only been exploring for three and already I can't tell one from the next."

Ronon scoffed. "Were you ever able to?"

Rodney glanced over his shoulder at him before irately facing forward again. "Ha-ha, very funny. My point is Dr. Jackson's coming to Atlantis to visit Sam and learn more about the city, not to explore other worlds." He paused to interpret the scanner's readings and then shrewdly eyed the group's commanding officer. "If you're thinking what I think you're thinking, the answer's no."

Sheppard opened his mouth, somewhat staggered by the scientist's assertion. When Rodney turned away to start down a side road, he followed in mild offense. "I resent that, McKay. You've no way of knowing what I'm thinking."

"You're thinking of using Dr. Jackson's diplomatic expertise to make contact with the people of this world to see just how advanced their technology is in order to find some other means of combating the Wraith," Rodney said with his typical flippancy. "Obviously, from what we've detected, these people have managed to build an impressive civilization despite the Cullings and since we've already deduced they don't need the power source we're after, they must be utilizing something we've yet to come across. Alien weapons, shields, that sort of thing. You want Dr. Jackson to help us negotiate for them."

Bemused, Teyla and Ronon glanced at each other while Sheppard rigidly defended himself. "Honestly, McKay, could you try sounding a little less patronizing? I would've thought you'd be the one eager to get your hands on new technology."

"I'm always eager to get my hands on new technology," Rodney assured him as they came to a colossal structure, three stories high with more stone pillars lining each of the outer galleries. A set of old, cracked stairs led to the building's entrance and they started up without a moment's hesitation. "Unfortunately," Rodney continued, "I wouldn't rely on Dr. Jackson in a case like this. There's no question he's the best, but he can't be bothered with interplanetary negotiations anymore. It'd be like asking… like asking Indiana Jones to waste his time and talents moderating between two museums who both want the same exhibit."

Sheppard smiled, always pleased with the allusions he knew Ronon and Teyla wouldn't understand. "Yes, but Indiana Jones wouldn't be wasting his time if the museums started shooting each other, right? We already agreed advanced civilizations with no knowledge of the Stargate aren't necessarily going to be open to the idea of aliens, so wouldn't you rather it be Dr. Jackson making first contact than someone else like, let's say, Richard Woolsey?"

"Do I even need to dignify that with a response?" Rodney asked as they reached the top of the stairs and made their way into an enormous, empty entrance hall. The lighting was dim, despite the sunbeams pouring in through the windows and gaps that had formed over centuries in the crumbling walls. With their arrival, dust that had long since settled on the ground billowed upwards, but not so much to be a hindrance. If anything, it merely gave the place a more mysterious, fantastic ambiance, not that Rodney or anyone else on the team could fully appreciate it. After all, they were no archeologists. Rodney continued forward without giving the scene so much as a second glance. "In any case, the point still stands: General O'Neill doesn't want Dr. Jackson put deliberately in harm's way."

"General O'Neill?" Sheppard frowned, inadvertently picturing the crabby, albeit legendary hero who had both recruited him for the Atlantis expedition _and_ threatened to fire him back when they'd rescued both each other and the city from the Replicators. He was certainly not a man anyone wanted to cross, and yet… "What say does he have in it? Landry's the one running the SGC."

Rodney stopped short, clearly caught up in the conversation, so much so that he actually seemed to have forgotten about the power source, however temporarily. "General O'Neill is one of the most influential men in two galaxies. I can remember, when we first set out on the Atlantis expedition, no one, and I mean no one, was more eager to go than Dr. Jackson. And even today, after all this time, he's still the foremost expert on all things Ancient. So why's he only been to Atlantis once? Because General O'Neill's been pulling teeth to keep him in the Milky Way. Of course, the fight with the Ori hasn't helped Dr. Jackson's case, it's been keeping him busy, but the Pegasus Galaxy is still the last place General O'Neill wants him and he's got no qualms about saying so."

"You seem to be well informed in this matter, Rodney," Teyla observed, to which the scientist glanced down at his scanner, slightly flustered. Ronon couldn't help but smirk; watching McKay stammer was always entertaining and so he leaned back with crossed arms to enjoy the show.

"Yes, well…" Rodney scratched his nose. "I personally appealed to General O'Neill three years ago to allow Dr. Jackson on the expedition. When he refused…"

Sheppard could already guess the answer. "When he refused, you ceaselessly pestered him until he gave you an explanation to shut you up." The look on Rodney's face was confirmation enough.

Ronon raised an eyebrow. "You actually requested someone other than yourself?"

"Well, it's been known to happen," Rodney snapped, irritation rapidly crossing his countenance. "Most of the expedition is run by civilians and with the notable exception of myself, Dr. Jackson's the most competent of the lot. Besides, he's the only one truly qualified to be exploring Atlantis in the first place. You'd be an idiot not to want him." And with that, Rodney turned his attention back to his scanner and started towards the far side of the entrance hall. Sheppard, Ronon, and Teyla trailed after him thoughtfully.

They didn't stop until they reached the back wall, which was covered entirely, from floor to ceiling, in both pictures and writing. Low relief. The first hint of a heritage in this forgotten city. They had finally found something an archeologist might make heads or tails of and they didn't even have an archeologist on hand. It would have been a shame had any of them, aside from Teyla, actually cared about anything other than completing their mission.

"Am I getting this right?" Ronon asked abruptly, perhaps the most uninterested in their discovery. He turned towards Sheppard while Rodney looked back and forth from the wall to his scanner, probing meticulously for clues and further direction towards their target. "We're sneaking onto a planet, we're stealing a power source, we're going back to Atlantis to welcome this Dr. Jackson guy to the city, who won't be negotiating with the people of this world, even though we need to negotiate with them and he's the most qualified man for the job, just because O'Neill's overprotective?"

Sheppard glanced from the wall to Ronon and back again. "Sounds about right."

"Then I've just got one question."

The man's voice was as husky and dangerous as ever. While Rodney, again, took no notice, Sheppard met Teyla's gaze warily. She still wasn't pleased with their objective and now they had a potentially violent Satedan to keep under control. You could never tell just what Ronon was thinking and though Sheppard trusted him with his life, there were times when he worried about the man's recklessness. "Which is?"

Ronon glowered. "Who the hell's Indiana Jones?"

"Oh my god," Rodney said before a slightly relieved Sheppard could enlighten his comrade. He backed away from the wall, looking up at it as if trying to take it all in at once. "This is… this is… oh my god…"

"Rodney?" Sheppard asked, facing the scientist while Teyla stepped towards him in concern. He looked like he was staring at a ghost; his face was pale and clammy, he was trembling, and when he locked eyes on the colonel, the windows to his soul were flooded with astonishment.

"I think we're going to need Dr. Jackson after all."

**ooooooo**

Cheers!


End file.
